I have just installed gentoo with gnome/systemd and after few times of very well booting and working with gnome...
Now I am facing with extremely slow booting and working with gnome - every action takes a lot of time.
My intuition is that this problem has not to do with gentoo or gnome, but with bios or Hard Drive -
However I am not sure and need your advise how to handle this issue?

EDIT: In addition - when I try to go into bios setup (by enter Del) it also takes a lot of time -
If my HDD close to the edge - Is there some tools for analyzing/fixing? How to backup the system?

Last edited by pmam on Mon Apr 14, 2014 7:26 am; edited 4 times in total

Have you already checked if your filesystem is in a consistent state, with tools like fsck.foo?
Have you setup its automatically usage correct into your fstab?

If your BIOS has an option for activating SMART, enable it. Only then it will automatically remap defect blocks.
This was two times the root cause for exactly the behaviour you describe, once on my machine and once of a PC of a colleague.

If you have a hard drive defect which couldn't be fixed by smart, we'll see it, if you do a self test of your drive using this command:
Eventually you have to install the package smartmontools.

Code:

smartctl -t short /dev/sdx

Wait at least a minute until its finished.

Check and interpret the output of its results with:

Code:

smartctl --all /dev/sdx

If you're unsure or not able to do, post your results.

Much success, Andy._________________If you want to see a Distro done right, compile it yourself!

Do you see any messages of concern in the output of `dmesg` or `journalctl -rb`? If you `emerge dev-util/perf` and run `perf top` as root; do you see anything of concern there? Take note of the amount of irqs/sec in the top left corner, as well as the amount of percent time spent in the kernel next to it; for the rest of it you'll want to look for lines that are abnormally high (marked in red) as well as libraries that are present too often (marked in green). If possible, feel free to provide a copy; such that we can provide you more specific advice.

EDIT: In addition: when I try to go into bios setup (by enter Del) it also takes a lot of time.

A bad hdd can take time to answer, so if you hit del and need time to enter your bios, look at where it get stuck, if it's to detect hdd, you don't really need any program to tell you it isn't in healthy state.

My BIOS HDD SMART capability is already activated- I do not think it helps...

I installed 'smartmontools' and run this command: 'smartctl -t short /dev/sda' and here the results:
EDIT: After running this command it looks much faster but I am not sure it solve all problems...
Now there is a strange issue: The icons of Gnome menu disappear suddenly -
I do not know if it has to do with the HDD problem or with Gnome installation?

The following keyword changes are necessary to proceed:
(see "package.accept_keywords" in the portage(5) man page for more details)
# required by dev-util/perf (argument)
=dev-util/perf-3.13.1-r1 ~amd64

Use --autounmask-write to write changes to config files (honoring
CONFIG_PROTECT). Carefully examine the list of proposed changes,
paying special attention to mask or keyword changes that may expose
experimental or unstable packages.

See the output, you can run the emerge with --autounmask-write and then run either etc-update or dispatch-conf to review the changes to your config files; alternatively, manually copy the =dev-util/perf-3.13.1-r1 ~amd64 line into /etc/portage/package.accept_keywords and then you can proceed to emerge perf again.

No, nothing of concern; libvte, libc and perf are the result of perf itself monitoring. The rest is all under 4% and even most under 2% which means there is nothing specific there taking up a large amount of time.

You might have missed it earlier; but I think there might be something in the logs indicating a problem, do you see any messages of concern in the output of `dmesg` or `journalctl -rb`? I'd expect a message about a GPE storm, a flood or something that shows there are high number of interrupts or timeouts happening; but it could be anything, hopefully it will be in the logs (if not, we'll need to look for more in-depth troubleshooting techniques).

could be that your fstab is missing these two lines, but I'm not fully sure if these are needed these newer days, or if they are activated in the background.
For this case, you should see them nevertheless in the output of mount on cml.

none /proc proc defaults 0 0
none /dev/shm tmpfs defaults 0 0

Rest seems to be right, especially the fsck value for your root enty, so it would be checked before mounting it.
Yo could check it manually via fsck.ext4 /dev/sda4, but it will only work if the devices isn't mounted. So you have to run it from an other system/live system, but it seems not to be necessary cause your right values in your fstab.

You told that your drive works faster now, which state my intention was right, to point you into this direction.
Nevertheless, the smart values of your drive tells me, that your data are not reliable any longer.
You should do a backup, if you have none, also if it could take eventually month until its completely broken.
Nobody could forecast it exactly, and its only a snapshot of this moment.
It gets more precise if someone tracks the changes over the time, but your hard drive seems to have a problem, if I interpret the values right.

So If you have a second one, clone it and try to work at this one, to check if it would fix your problems.

Much success, Andy.

pmam wrote:

Hi all of you guys,

THanks for your helpful responses!

Dear Randy & Splink - I am not familiared with fsck.foo - How to use it - what the exact command?

My BIOS HDD SMART capability is already activated- I do not think it helps...

I installed 'smartmontools' and run this command: 'smartctl -t short /dev/sda' and here the results:
EDIT: After running this command it looks much faster but I am not sure it solve all problems...
Now there is a strange issue: The icons of Gnome menu disappear suddenly -
I do not know if it has to do with the HDD problem or with Gnome installation?

_________________If you want to see a Distro done right, compile it yourself!

If I can get a conclusion and summarize all this topic, I figure out that my HDD is going to die and I need to replace it!
However, just before it will go to recycling, I would like to know if there is any Linux tool to perform analyzing
and marking the bad sectors ( I think that windows has something like that, I am not sure...) -
So may be there is a chance one of million to save our lovely earth from facing with my full of chemicals HDD...

Anyway - Please let me know how to make backup or clone?
I am not familiar with those but assume that clone make an 'image' from the old HDD,
so after replacing HDD, I can do a simple copy ,without re-installation, and get the same system and data again.
BTW - How can I copy this clone after replacing HDD? On another computer or with live DOK?
Also - if I decide to reinstall gentoo on the new HDD - I guess this is your recommendation - how to backup the data? -
There is a special tool or just copy the home directory?

rsync is nice, just make sure that you copy the extra file metadata as well (look into options like -a, -H, -A, -X); when ran a second time, it will check the date and size of all files to see if they are copied over correctly. It is also possible to have it compare the checksums; though, that might make a much longer time. It also has an --exclude parameter if you want to exclude certain things. And a lot of parameters for almost everything that you would want to do with it.

As for what to copy, you'll want to do some research about what all the directories do; some directories are important (eg. /var/db/pkg/ is needed if you want to have a full copy, but not if you do a reinstall), others not so much (eg. /var/log/). Definitely important are /etc/ (your configuration), /home/ (your data), /root/ (also your data) and /var/lib/portage/world (selected packages) and perhaps other certain directories under /var/. It is not guaranteed that this last list is complete; so, walk down some levels deep into several directories about what you want and don't want to copy.

I'm not great systemd/gnome fan, but can you swap topic so others systemd/gnome users won't fall on it?
Your hdd was certainly on the line, and emerging the package have certainly push it to its end, but it's not really those package's fault.

If I can get a conclusion and summarize all this topic, I figure out that my HDD is going to die and I need to replace it!
However, just before it will go to recycling, I would like to know if there is any Linux tool to perform analyzing
and marking the bad sectors ( I think that windows has something like that, I am not sure...) -

That's what the short smart testool had already done, including remapping of the bad blocks to good reserve blocks, but you could do it deeper using the long test instead:

smartctl -t long /dev/sdx
But cause it will take some hours, the risk increase that your hard drive could fully die. That's why I recommend to do a backup first.
Windows or drive manufacturer specific tools don't do it better mostly, but these are less strictly in judging a hard drive as defect to lower the warranty claims, until it is really broken.

pmam wrote:

Anyway - Please let me know how to make backup or clone?
I am not familiar with those but assume that clone make an 'image' from the old HDD,
so after replacing HDD, I can do a simple copy ,without re-installation, and get the same system and data again.
BTW - How can I copy this clone after replacing HDD? On another computer or with live DOK?
Also - if I decide to reinstall gentoo on the new HDD - I guess this is your recommendation - how to backup the data? -
There is a special tool or just copy the home directory?

Thanks

No need to reinstall Gentoo again, if you copy over all your data right. But there are so many ways how to do it, that its hard to describe the one that is the best for your scenario, cause we don't know your requirements.

It takes me too long today, to give you a course in how to clone your system in the way you need it, especially without knowing it deeply.
Some month ago I wrote an article for a magazine, which explains all the basics in learning how to do it, so I know now how much work it could be.
The problem with this, its in German language only, so I guess its no help for you.
Eventually some of the other guys here, could refer to a similar documentation in English.

In my opinion its not enough to recommend you tools like clonezilla, but it could be a good first starting point to make life easier for you.
Once you know what's the best strategy for your needs is, connect a new drive to your pc, start from a live CD, than start to cloneing/partitioning/copying your drive/date to the new target.

Much success,

Andy._________________If you want to see a Distro done right, compile it yourself!

I thought it is less complicated to describe howto clone...
However, what you wrote help me to figure out what and where to look for in order to get a proper backup -
sometimes it is quite much to tell someone that it is not simple as he thought, so he will take care...

Quote:

The problem with this, its in German language only, so I guess its no help for you.

If I will follow the output of Google Translator for your article... I would have an interesting clone

I will learn about clonezilla, as you recommend for the starting point,
and TomWij recommend on rsync - I will try to see how to do it.
From these tools I hope to have enough information.

Krinn Hi,

Sorry but I think I do not understand your post -
Do you think that the failure of the HDD has to do with installing gnome/systemd?
Consequently, you want me to swap (I do not know how to do it...) this topic to the DE forum?
If yes - I do not think that there is a connection between the bad HDD to systemd/gnome -
But I am a gentoo's beginner, so maybe one of the senior participants in this topic,
would advise regarding this issue, and I will do what is needed to do...

I believe they are asking if you could edit the title of your topic (this topic) to something that more accurately describes the now-revealed issue, so as to not have it lure in users seeking for Gnome/systemd-specific help.

I'd perhaps at least add a [Solved] 'tag' as is customary, and perhaps a note about the HDD coming to a foul end so that readers can easily see that it was hardware related.

To do that, you need only edit the first post of yours, and the subject-line therein. ^^

It's always nasty to lose a drive.

Hopefully the next one will last longer!_________________Kind Regards,
~ The Noob Unlimited ~

Yes, now I understand your constructive posts - I edited my topic subject and first post -
I hope it is more clear and will help the next poor bad HDD owners...
However, if you think it is not clear enough, please let me know and I will try my best.

And for your hdd, you can live well with some bad sectors, mark them to not use them anymore and it's ok.
But your problem is worst : hdd slow at answering bios mean the hdd is really in bad state. This time marking bad sectors won't help, you're hdd is dying.
It's easy, in FAT you mark bad sectors, some fs allow to use a copy, else if FAT is damage, your dead.
But bios doesn't care about FAT area, but about MBR, if that one is damage. You have no choice than change disk.

As i said, if your bios takes time with your hdd...
Your best option is stop using it, so you preserve it until you're ready for backup.

I thought it is less complicated to describe howto clone...
However, what you wrote help me to figure out what and where to look for in order to get a proper backup -
sometimes it is quite much to tell someone that it is not simple as he thought, so he will take care...

Quote:

The problem with this, its in German language only, so I guess its no help for you.

If I will follow the output of Google Translator for your article... I would have an interesting clone

Ok pmam, good idea. I never used google translater before, but if you're willing to try to read and follow it, give it a try and we'll see if you get an interesting clone afterwards.
I'm curious about it, if its really readable and if it make sense, but it should be better if I try to translate such a complex text. You'll find it here:

I thought it is a semi-joke, however after reading the first paragraph, it seems quite readable and make sense -
It is automatically translated to English without my intervention - may be you defined it before...
We should take advantage of technology (not just suffer from the disadvantages!) - In case it is really working...
I will try to follow and let you know the interesting result...